ArticleBiophysical journal2021
Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- Conserved structural features of RNA export pores spanning the double membrane of arterivirus and coronavirus replication organelles.Journal of virology · 2026Article
- Evaluation of dead-end hollowfiber ultrafilter options for enumerating somatic and F+ coliphage in ambient waters and wastewater.Journal of virological methods · 2026Article
- Biochemical and functional characterization of orf virus decapping protein OV71.Virology journal · 2025Article
- Material-to-Application Integration: Rapid Fabrication of Field-Deployable Hydrogel-SiOAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The comparison of decay rates of infectious SARS-CoV-2 and viral RNA in environmental waters and wastewater.The Science of the total environment · 2024Article
- Solvation-Enhanced Salt Bridges.Journal of the American Chemical Society · 2024Article
- Comparing the decay of human wastewater-associated markers and enteric viruses in laboratory microcosms simulating estuarine waters in a temperate climatic zone using qPCR/RT-qPCR assays.The Science of the total environment · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Sequence- and structure-specific RNA oligonucleotide binding attenuates heterogeneous nuclear ribonucleoprotein A1 dysfunction.Frontiers in molecular biosciences · 2023Article
- Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides.Journal of chemical information and modeling · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.